Loss of hearing and balance is a widespread and debilitating medical condition in humans, and is predominantly caused by a loss of hair cells, the primary sensory cell of the inner ear. Hair cells do not naturally regenerate in humans, in contrast to other animals such as zebrafish where hair cells readily regenerate. To understand hair cell formation during development and hair cell regeneration in response to damage we will undertake an integrative systems biology based approach. Our approach integrates in toto imaging which provides systematic high resolution analysis across the space and time of hair cell generation with omic approaches that allow systematic analysis of transcriptional activity across the genome. Specifically, we will use in toto imaging, a technology we developed, to generate a 4-dimensional, cell-based Digital Ear that comprehensively quantifies the cellular processes that form and regenerate hair cells in zebrafish. We will use cell-type-specific ChIP-seq of histone modifications to determine the enhancers, promoters, and insulators active across the entire genome at all the key steps of hair cell generation. Bioinformatic approaches will be used to map transcription factor binding sites within defined enhancers to the genes they control to construct a comprehensive cis-regulatory network within the virtual cells of our Digital Ear. This research will provide unprecedented insight into how the genome encodes the stepwise specification of hair cells, with potentially important implications for hair cell regeneration in humans. Relevance to Health Deficiencies in hearing and balance are widespread and debilitating. They are principally caused by loss of the sensory cells (hair cells) of the inner ear hair which cannot regenerate in humans but can in other animals. We seek to understand the genetic and cellular control of inner ear hair cell regeneration. PUBLIC HEALTH RELEVANCE: Deficiencies in hearing and balance are widespread and debilitating. They are principally caused by loss of the sensory cells (hair cells) of the inner ear hair which cannot regenerate in humans but can in other animals. We seek to understand the genetic and cellular control of inner ear hair cell regeneration.